Mapping Heat Resistance in YeastsIn a proof-of-concept study, researchers demonstrated that a new genetic mapping strategy called RH-Seq can identify genes that promote heat resistance in the yeast Saccharomyces cerevisiae, allowing this species to grow better than its closest relative S. paradoxus at high temperatures.

First Monoploid Reference Sequence of SugarcaneFor the highly polyploid sugarcane, an international team of researchers has successfully assembled a first monoploid reference sequence using a targeted approach that focused on the gene rich part of the genome by harnessing information from a sequenced related species – sorghum.

Defining a Pan-Genome for Antarctic ArchaeaSome Antarctic lakes have salinities 10 times that of seawater. By collecting and sequencing dominant haloarchaeal sequences from six hypersaline lakes, researchers focused on understanding the genomic variation in haloarchaea across East Antarctica.

Methane Flux in the AmazonWetlands are the single largest global source of atmospheric methane. This project aims to integrate microbial and tree genetic characteristics to measure and understand methane emissions at the heart of the Amazon rainforest.

Insights into Functional Diversity in NeurosporaThis proposal investigates the genetic bases of fungal thermophily, biomass-degradation, and fungal-bacterial interactions in Sordariales, an order of biomass-degrading fungi frequently encountered in compost and encompassing one of the few groups of thermophilic fungi.

Mining IMG/M for CRISPR-Associated ProteinsResearchers report the discovery of miniature CRISPR-associated proteins that can target single-stranded DNA. The discovery was made possible by mining the datasets in the Integrated Microbial Genomes and Microbiomes (IMG/M) suite of tools managed by the JGI. The sequences were then biochemically characterized by a team led by Jennifer Doudna’s group at UC Berkeley.

DAS Tool for Genome Reconstruction from MetagenomesThrough the JGI’s Emerging Technologies Opportunity Program (ETOP), researchers have developed and improved upon a tool that combines existing DNA sequence binning algorithms, allowing them to reconstruct more near-complete genomes from soil metagenomes compared to other methods. The work was published in Nature Microbiology.

Preparing for a Sequence Data DelugeThe approved CSP 2019 proposals leverage new capabilities and higher throughput in DNA sequencing, synthesis and metabolomics. Additionally, just over half of the accepted proposals come from primary investigators who have never led any previously accepted JGI proposal.

Innovative Technology Improves Our Understanding of Bacterial Cell SignalingCyclic di-GMP (Guanine Monophosphate) is found in nearly all types of bacteria and interacts with cell signaling networks that control many basic cellular functions. To better understand the dynamics of this molecule, researchers developed the first chemiluminescent biosensors for measuring cyclic di-GMP in bacteria through work enabled by the JGI’s Community Science Program (CSP).

Expanding Fungal Diversity, One Cell at a TimeIn Nature Microbiology, a team led by JGI researchers has developed a pipeline to generate genomes from single cells of uncultivated fungi. The approach was tested on several uncultivated fungal species representing early diverging fungi.

Evolutionary Changes in the Genetic Code of YeastsIn nuclear genomes, a genetic code change where the amino acid assignment of a sense codon is swapped for a different amino acid is very rare. In a Nature Communications that built on a 2016 JGI PNAS study, researchers looked at the genomes of 52 yeast species, including seven newly sequenced and observed all three CUG codon reassignments: CUG-Ser, CUG-Ala, and CUG-Leu.

Celebrating the JGI-UC Merced Genomics Internship ProgramOriginally conceived as a graduate student summer research experience at the JGI, the Genomics Internship Program expanded to include UC Merced undergraduate students through the California Alliance for Minority Participation (CAMP) program. Since 2014, more than 20 UC Merced students have contributed to the research of 13 JGI scientists.

Developing a thermophilic fungal model group

Thermophilic fungi have been an important source of industrial enzymes for decades but research and development efforts have historically focused on the identification and characterization of cellulolytic genes from just a few strains. This approach has produced advanced enzymes over time, but recent genomics-based investigation has almost instantaneously yielded a diverse palette of novel, thermostable, high efficiency gene products that can be mixed and matched to improve existing enzyme cocktails or generate cocktails de novo. Thermophilic fungi likely have unique, but as yet largely uncharacterized roles in the global carbon cycle because they possess optimal growth temperatures (45-55 °C) well above those of the vast majority of microorganisms. The researchers are interested in developing a Chaetomiaceae phylogenomics program to investigate the molecular basis of fungal thermophily and to provide an empirical framework for linking genotype and phenotype, in part to understand the molecular basis of fungal thermophily and advance understanding of fungal ecology.